We present Denario, an AI multi-agent system designed to serve as a scientific research assistant. Denario can perform many different tasks, such as generating ideas, checking the literature, developing research plans, writing and executing code, making plots, and drafting and reviewing a scientific paper. The system has a modular architecture, allowing it to handle specific tasks, such as generating an idea, or carrying out end-to-end scientific analysis using Cmbagent as a deep-research backend. In this work, we describe in detail Denario and its modules, and illustrate its capabilities by presenting multiple AI-generated papers generated by it in many different scientific disciplines such as astrophysics, biology, biophysics, biomedical informatics, chemistry, material science, mathematical physics, medicine, neuroscience and planetary science. Denario also excels at combining ideas from different disciplines, and we illustrate this by showing a paper that applies methods from quantum physics and machine learning to astrophysical data. We report the evaluations performed on these papers by domain experts, who provided both numerical scores and review-like feedback. We then highlight the strengths, weaknesses, and limitations of the current system. Finally, we discuss the ethical implications of AI-driven research and reflect on how such technology relates to the philosophy of science. We publicly release the code at https://github.com/AstroPilot-AI/Denario. A Denario demo can also be run directly on the web at https://huggingface.co/spaces/astropilot-ai/Denario, and the full app will be deployed on the cloud.

A new research project, Plant Futures, envisions how a flower might respond to climate change over time. The Circaea alpina flower is modeled in software and its features transform algorithmically, according to how each is influenced by the changing climate data year by year. Flowers play a key role in most landscapes, from urban to rural areas. There might be dandelions poking through the cracks in the pavement, wildflowers on the highway median, or poppies covering a hillside. We might notice the time of year they bloom and connect that to our changing climate. Perhaps we are familiar with their cycles: bud, bloom, wilt, seed.

In this interview series, we're meeting some of the AAAI/SIGAI Doctoral Consortium participants to find out more about their research. In this latest interview, we hear from Flávia Carvalhido who is a PhD student at the University of Porto. We find out about her work on responsible multimodal AI, what inspired her to study AI, and how she found the Doctoral Consortium experience. My PhD programme is on Informatics Engineering in the Faculty of Engineering at the University of Porto, where I also got both my Bachelor's and Master's in the same field. My thesis research project is focused on responsible multimodal AI, titled "Stress Testing of Image-Text Multimodal Models in Medical Image Report Generation", supervised by Professor Henrique Lopes Cardoso and Professor Vítor Cerqueira and developed in the LIACC research laboratory.

This paper describes the design, implementation and use of a new UML modeling tool that represents a significant advance over conventional tools. Among other things, it allows the integration of class diagrams and object diagrams as well as the execution of objects. This not only enables new software architectures characterized by the integration of software with corresponding object models, but is also ideal for use in teaching, as it provides students with a particularly stimulating learning experience. A special feature of the project is that it has emerged from a long-standing international research project, which is aimed at a comprehensive multi-level architecture. The project is therefore an example of how research can lead to valuable results that arise as a side effect of other work.

The increasing complexity of computer science research projects demands more effective tools for deploying code repositories. Large Language Models (LLMs), such as Anthropic Claude and Meta Llama, have demonstrated significant advancements across various fields of computer science research, including the automation of diverse software engineering tasks. To evaluate the effectiveness of LLMs in handling complex code development tasks of research projects, particularly for NLP/CV/AI/ML/DM topics, we introduce CSR-Bench, a benchmark for Computer Science Research projects. This benchmark assesses LLMs from various aspects including accuracy, efficiency, and deployment script quality, aiming to explore their potential in conducting computer science research autonomously. We also introduce a novel framework, CSR-Agents, that utilizes multiple LLM agents to automate the deployment of GitHub code repositories of computer science research projects. Specifically, by checking instructions from markdown files and interpreting repository structures, the model generates and iteratively improves bash commands that set up the experimental environments and deploy the code to conduct research tasks. Preliminary results from CSR-Bench indicate that LLM agents can significantly enhance the workflow of repository deployment, thereby boosting developer productivity and improving the management of developmental workflows.

This research-in-progress paper presents a new project management framework that utilises GenAI technology. The framework is designed to address the common challenge of uniform team compositions in academic and research project teams, particularly in universities and research institutions. It does so by integrating sociologically identified patterns of successful team member personalities and roles, using GenAI agents to fill gaps in team dynamics. This approach adds an additional layer of analysis to conventional project management processes by evaluating team members' personalities and roles and employing GenAI agents, fine-tuned on personality datasets, to fill specific team roles. Our initial experiments have shown improvements in the model's ability to understand and process personality traits, suggesting the potential effectiveness of GenAI teammates in real-world project settings. This paper aims to explore the practical application of AI in enhancing team diversity and project management

This paper presents HyperGraphOS, an innovative Operating System designed for the scientific and engineering domains. It combines model based engineering, graph modeling, data containers, and computational tools, offering users a dynamic workspace for creating and managing complex models represented as customizable graphs. Using a web based architecture, HyperGraphOS requires only a modern browser to organize knowledge, documents, and content into interconnected models. Domain Specific Languages drive workspace navigation, code generation, AI integration, and process organization.The platform models function as both visual drawings and data structures, enabling dynamic modifications and inspection, both interactively and programmatically. HyperGraphOS was evaluated across various domains, including virtual avatars, robotic task planning using Large Language Models, and meta modeling for feature based code development. Results show significant improvements in flexibility, data management, computation, and document handling.

The diagnostic imaging departments are under great pressure due to a growing workload. The number of required scans is growing and there is a shortage of qualified labor. AI solutions for medical imaging applications have shown great potential. However, very few diagnostic imaging models have been approved for hospital use and even fewer are being implemented at the hospitals. The most common reason why software projects fail is poor requirement engineering, especially non-functional requirements (NFRs) can be detrimental to a project. Research shows that machine learning professionals struggle to work with NFRs and that there is a need to adapt NFR frameworks to machine learning, AI-based, software. This study uses qualitative methods to interact with key stakeholders to identify which types of NFRs are important for medical imaging applications. The study was done on a single Danish hospital and found that NFRs of type Efficiency, Accuracy, Interoperability, Reliability, Usability, Adaptability, and Fairness were important to the stakeholders. Especially Efficiency since the diagnostic imaging department is trying to spend as little time as possible on each scan.

Research ideation involves broad exploring and deep refining ideas. Both require deep engagement with literature. Existing tools focus primarily on idea broad generation, yet offer little support for iterative specification, refinement, and evaluation needed to further develop initial ideas. To bridge this gap, we introduce IdeaSynth, a research idea development system that uses LLMs to provide literature-grounded feedback for articulating research problems, solutions, evaluations, and contributions. IdeaSynth represents these idea facets as nodes on a canvas, and allow researchers to iteratively refine them by creating and exploring variations and composing them. Our lab study (N=20) showed that participants, while using IdeaSynth, explored more alternative ideas and expanded initial ideas with more details compared to a strong LLM-based baseline. Our deployment study (N=7) demonstrated that participants effectively used IdeaSynth for real-world research projects at various ideation stages from developing initial ideas to revising framings of mature manuscripts, highlighting the possibilities to adopt IdeaSynth in researcher's workflows.

Advanced artificial intelligence (AI) systems with access to millions of research papers could inspire new research ideas that may not be conceived by humans alone. However, how interesting are these AI-generated ideas, and how can we improve their quality? Here, we introduce SciMuse, a system that uses an evolving knowledge graph built from more than 58 million scientific papers to generate personalized research ideas via an interface to GPT-4. We conducted a large-scale human evaluation with over 100 research group leaders from the Max Planck Society, who ranked more than 4,000 personalized research ideas based on their level of interest. This evaluation allows us to understand the relationships between scientific interest and the core properties of the knowledge graph. We find that data-efficient machine learning can predict research interest with high precision, allowing us to optimize the interest-level of generated research ideas. This work represents a step towards an artificial scientific muse that could catalyze unforeseen collaborations and suggest interesting avenues for scientists.